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NVlabs / nvbio

NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.
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make -j8 does not complete in Ubuntu 14.04 #11

Closed CnrLwlss closed 8 years ago

CnrLwlss commented 8 years ago

Hi,

I'm very interested to try out the CUDA accelerated version of bowtie2.

I haven't had any success compiling nvbio on my 64-bit Ubuntu workstation. make -j8; fails with cryptic message Error 2. I've copied the end of the error logs below.

I seem to have CUDA installed and in my path. I have not tried to enable nvidia display drivers for my Tesla GPGPU. I'm not sure what to do next.

Regards,

CONOR.


/home/conor/nvbio/contrib/htslib/htslib/bgzf.h(49): warning: signed bit field of length 1

/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
          detected during:
            instantiation of class "nvbio::iterator_system<iterator> [with iterator=D_StreamDNA]"
/home/conor/nvbio/nvbio/strings/string_set.h(487): here
            instantiation of class "nvbio::ConcatenatedStringSet<StringIterator, OffsetIterator> [with StringIterator=D_StreamDNA, OffsetIterator=nvbio::uint64 *]"
/home/conor/nvbio/nvMicroAssembly/kmers.h(40): here
            instantiation of class "D_KmerSet<string_set_type> [with string_set_type=D_SequenceSet]"
/home/conor/nvbio/nvMicroAssembly/assembly_graph_inl.h(284): here

/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
          detected during:
            instantiation of class "nvbio::iterator_system<iterator> [with iterator=nvbio::PackedStream<thrust::device_ptr<nvbio::uint32>, nvbio::uint8, 1U, true, nvbio::uint32>]"
/home/conor/nvbio/nvbio/strings/wavelet_tree.h(80): here
            instantiation of class "nvbio::WaveletTree<BitStreamIterator, IndexIterator, SymbolType> [with BitStreamIterator=nvbio::PackedStream<thrust::device_ptr<nvbio::uint32>, nvbio::uint8, 1U, true, nvbio::uint32>, IndexIterator=thrust::detail::normal_iterator<thrust::device_ptr<nvbio::uint32>>, SymbolType=nvbio::uint8]"
/home/conor/nvbio/nvbio-test/wavelet_test.cu(106): here

/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
          detected during:
            instantiation of class "nvbio::iterator_system<iterator> [with iterator=thrust::device_ptr<nvbio::uint32>]"
/home/conor/nvbio/nvbio/basic/packedstream_inl.h(1414): here
            instantiation of "void nvbio::assign(IndexType, InputIterator, nvbio::PackedStream<InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType>) [with InputIterator=thrust::transform_iterator<nvbio::select_bit_functor<nvbio::uint8>, thrust::detail::normal_iterator<thrust::device_ptr<nvbio::uint8>>, thrust::use_default, thrust::use_default>, InputStream=thrust::device_ptr<nvbio::uint32>, Symbol=nvbio::uint8, SYMBOL_SIZE_T=1U, BIG_ENDIAN_T=true, IndexType=nvbio::uint32]"
/home/conor/nvbio/nvbio/strings/wavelet_tree_inl.h(197): here
            instantiation of "void nvbio::setup(index_type, const string_iterator &, nvbio::WaveletTreeStorage<system_tag, index_type, symbol_type> &) [with system_tag=nvbio::device_tag, string_iterator=thrust::detail::normal_iterator<thrust::device_ptr<nvbio::uint8>>, index_type=nvbio::uint32, symbol_type=nvbio::uint8]"
/home/conor/nvbio/nvbio-test/wavelet_test.cu(97): here

/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
          detected during:
            instantiation of class "nvbio::iterator_system<iterator> [with iterator=nvbio::PackedStream<thrust::device_ptr<const nvbio::uint32>, nvbio::uint8, 1U, true, nvbio::uint32>]"
/home/conor/nvbio/nvbio/strings/wavelet_tree.h(80): here
            instantiation of class "nvbio::WaveletTree<BitStreamIterator, IndexIterator, SymbolType> [with BitStreamIterator=nvbio::PackedStream<thrust::device_ptr<const nvbio::uint32>, nvbio::uint8, 1U, true, nvbio::uint32>, IndexIterator=thrust::detail::normal_iterator<thrust::device_ptr<const nvbio::uint32>>, SymbolType=nvbio::uint8]"
/home/conor/nvbio/examples/waveletfm/waveletfm.cu(99): here

/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
          detected during:
            instantiation of class "nvbio::iterator_system<iterator> [with iterator=nvbio::PackedStream<thrust::device_ptr<nvbio::uint32>, nvbio::uint8, 1U, true, nvbio::uint32>]"
/home/conor/nvbio/nvbio/strings/wavelet_tree.h(80): here
            instantiation of class "nvbio::WaveletTree<BitStreamIterator, IndexIterator, SymbolType> [with BitStreamIterator=nvbio::PackedStream<thrust::device_ptr<nvbio::uint32>, nvbio::uint8, 1U, true, nvbio::uint32>, IndexIterator=thrust::detail::normal_iterator<thrust::device_ptr<nvbio::uint32>>, SymbolType=nvbio::uint8]"
/home/conor/nvbio/examples/waveletfm/waveletfm.cu(99): here

/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
          detected during:
            instantiation of class "nvbio::iterator_system<iterator> [with iterator=nvbio::PackedStream<thrust::device_ptr<const nvbio::uint32>, nvbio::uint8, 1U, true, nvbio::uint32>]"
/home/conor/nvbio/nvbio/strings/wavelet_tree.h(80): here
            instantiation of class "nvbio::WaveletTree<BitStreamIterator, IndexIterator, SymbolType> [with BitStreamIterator=nvbio::PackedStream<thrust::device_ptr<const nvbio::uint32>, nvbio::uint8, 1U, true, nvbio::uint32>, IndexIterator=thrust::detail::normal_iterator<thrust::device_ptr<const nvbio::uint32>>, SymbolType=nvbio::uint8]"
/home/conor/nvbio/nvbio/strings/wavelet_tree.h(343): here
            instantiation of "nvbio::WaveletTreeStorage<SystemTag, IndexType, SymbolType>::plain_view_type nvbio::plain_view(nvbio::WaveletTreeStorage<SystemTag, IndexType, SymbolType> &) [with SystemTag=nvbio::device_tag, IndexType=nvbio::uint32, SymbolType=nvbio::uint8]"
/home/conor/nvbio/nvbio-test/wavelet_test.cu(106): here

3 errors detected in the compilation of "/tmp/tmpxft_000021da_00000000-7_wavelet_test.cpp1.ii".
CMake Error at nvbio-test_generated_wavelet_test.cu.o.cmake:264 (message):
  Error generating file
  /home/conor/nvbio/build/nvbio-test/CMakeFiles/nvbio-test.dir//./nvbio-test_generated_wavelet_test.cu.o

make[2]: *** [nvbio-test/CMakeFiles/nvbio-test.dir/./nvbio-test_generated_wavelet_test.cu.o] Error 1
make[1]: *** [nvbio-test/CMakeFiles/nvbio-test.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
          detected during:
            instantiation of class "nvbio::iterator_system<iterator> [with iterator=thrust::device_ptr<nvbio::uint32>]"
/home/conor/nvbio/nvbio/basic/packedstream_inl.h(1414): here
            instantiation of "void nvbio::assign(IndexType, InputIterator, nvbio::PackedStream<InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType>) [with InputIterator=thrust::transform_iterator<nvbio::select_bit_functor<nvbio::uint8>, thrust::detail::normal_iterator<thrust::device_ptr<nvbio::uint8>>, thrust::use_default, thrust::use_default>, InputStream=thrust::device_ptr<nvbio::uint32>, Symbol=nvbio::uint8, SYMBOL_SIZE_T=1U, BIG_ENDIAN_T=true, IndexType=nvbio::uint32]"
/home/conor/nvbio/nvbio/strings/wavelet_tree_inl.h(197): here
            instantiation of "void nvbio::setup(index_type, const string_iterator &, nvbio::WaveletTreeStorage<system_tag, index_type, symbol_type> &) [with system_tag=nvbio::device_tag, string_iterator=nvbio::PackedStream<thrust::device_ptr<nvbio::uint32>, nvbio::uint8, 8U, true, nvbio::uint32>, index_type=nvbio::uint32, symbol_type=nvbio::uint8]"
/home/conor/nvbio/examples/waveletfm/waveletfm.cu(93): here

3 errors detected in the compilation of "/tmp/tmpxft_000021e5_00000000-7_waveletfm.cpp1.ii".
CMake Error at waveletfm_generated_waveletfm.cu.o.cmake:264 (message):
  Error generating file
  /home/conor/nvbio/build/examples/waveletfm/CMakeFiles/waveletfm.dir//./waveletfm_generated_waveletfm.cu.o

make[2]: *** [examples/waveletfm/CMakeFiles/waveletfm.dir/./waveletfm_generated_waveletfm.cu.o] Error 1
make[1]: *** [examples/waveletfm/CMakeFiles/waveletfm.dir/all] Error 2
1 error detected in the compilation of "/tmp/tmpxft_000021d2_00000000-7_haplotype_caller.cpp1.ii".
CMake Error at nvMicroAssembly_generated_haplotype_caller.cu.o.cmake:264 (message):
  Error generating file
  /home/conor/nvbio/build/nvMicroAssembly/CMakeFiles/nvMicroAssembly.dir//./nvMicroAssembly_generated_haplotype_caller.cu.o

make[2]: *** [nvMicroAssembly/CMakeFiles/nvMicroAssembly.dir/./nvMicroAssembly_generated_haplotype_caller.cu.o] Error 1
make[1]: *** [nvMicroAssembly/CMakeFiles/nvMicroAssembly.dir/all] Error 2
make: *** [all] Error 2
nsubtil commented 8 years ago

Which CUDA toolkit version are you building with? NVBIO will only build with CUDA 6.5 at the moment.

On Wed, Nov 4, 2015 at 7:40 AM, Conor Lawless notifications@github.com wrote:

Hi,

I'm very interested to try out the CUDA accelerated version of bowtie2.

I haven't had any success compiling nvbio on my 64-bit Ubuntu workstation. make -j8; fails with cryptic message Error 2. I've copied the end of the error logs below.

I seem to have CUDA installed and in my path. I have not tried to enable nvidia display drivers for my Tesla GPGPU. I'm not sure what to do next.

Regards,

CONOR.

/home/conor/nvbio/contrib/htslib/htslib/bgzf.h(49): warning: signed bit field of length 1

/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type" detected during: instantiation of class "nvbio::iterator_system [with iterator=D_StreamDNA]" /home/conor/nvbio/nvbio/strings/string_set.h(487): here instantiation of class "nvbio::ConcatenatedStringSet<StringIterator, OffsetIterator> [with StringIterator=D_StreamDNA, OffsetIterator=nvbio::uint64 *]" /home/conor/nvbio/nvMicroAssembly/kmers.h(40): here instantiation of class "D_KmerSet [with string_set_type=D_SequenceSet]" /home/conor/nvbio/nvMicroAssembly/assembly_graph_inl.h(284): here

/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type" detected during: instantiation of class "nvbio::iterator_system [with iterator=nvbio::PackedStreamthrust::device_ptr<nvbio::uint32, nvbio::uint8, 1U, true, nvbio::uint32>]" /home/conor/nvbio/nvbio/strings/wavelet_tree.h(80): here instantiation of class "nvbio::WaveletTree<BitStreamIterator, IndexIterator, SymbolType> [with BitStreamIterator=nvbio::PackedStreamthrust::device_ptr<nvbio::uint32, nvbio::uint8, 1U, true, nvbio::uint32>, IndexIterator=thrust::detail::normal_iteratorthrust::device_ptr, SymbolType=nvbio::uint8]" /home/conor/nvbio/nvbio-test/wavelet_test.cu(106): here

/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type" detected during: instantiation of class "nvbio::iterator_system [with iterator=thrust::device_ptrnvbio::uint32]" /home/conor/nvbio/nvbio/basic/packedstream_inl.h(1414): here instantiation of "void nvbio::assign(IndexType, InputIterator, nvbio::PackedStream<InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType>) [with InputIterator=thrust::transform_iteratornvbio::select_bit_functor<nvbio::uint8, thrust::detail::normal_iteratorthrust::device_ptr, thrust::use_default, thrust::use_default>, InputStream=thrust::device_ptrnvbio::uint32, Symbol=nvbio::uint8, SYMBOL_SIZE_T=1U, BIG_ENDIAN_T=true, IndexType=nvbio::uint32]" /home/conor/nvbio/nvbio/strings/wavelet_tree_inl.h(197): here instantiation of "void nvbio::setup(index_type, const string_iterator &, nvbio::WaveletTreeStorage<system_tag, index_type, symbol_type> &) [with system_tag=nvbio::device_tag, string_iterator=thrust::detail::normal_iteratorthrust::device_ptr, index_type=nvbio::uint32, symbol_type=nvbio::uint8]" /home/conor/nvbio/nvbio-test/wavelet_test.cu(97): here

/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type" detected during: instantiation of class "nvbio::iterator_system [with iterator=nvbio::PackedStream<thrust::device_ptr, nvbio::uint8, 1U, true, nvbio::uint32>]" /home/conor/nvbio/nvbio/strings/wavelet_tree.h(80): here instantiation of class "nvbio::WaveletTree<BitStreamIterator, IndexIterator, SymbolType> [with BitStreamIterator=nvbio::PackedStream<thrust::device_ptr, nvbio::uint8, 1U, true, nvbio::uint32>, IndexIterator=thrust::detail::normal_iterator<thrust::device_ptr>, SymbolType=nvbio::uint8]" /home/conor/nvbio/examples/waveletfm/waveletfm.cu(99): here

/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type" detected during: instantiation of class "nvbio::iterator_system [with iterator=nvbio::PackedStreamthrust::device_ptr<nvbio::uint32, nvbio::uint8, 1U, true, nvbio::uint32>]" /home/conor/nvbio/nvbio/strings/wavelet_tree.h(80): here instantiation of class "nvbio::WaveletTree<BitStreamIterator, IndexIterator, SymbolType> [with BitStreamIterator=nvbio::PackedStreamthrust::device_ptr<nvbio::uint32, nvbio::uint8, 1U, true, nvbio::uint32>, IndexIterator=thrust::detail::normal_iteratorthrust::device_ptr, SymbolType=nvbio::uint8]" /home/conor/nvbio/examples/waveletfm/waveletfm.cu(99): here

/home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type" detected during: instantiation of class "nvbio::iterator_system [with iterator=nvbio::PackedStream<thrust::device_ptr, nvbio::uint8, 1U, true, nvbio::uint32>]" /home/conor/nvbio/nvbio/strings/wavelet_tree.h(80): here instantiation of class "nvbio::WaveletTree<BitStreamIterator, IndexIterator, SymbolType> [with BitStreamIterator=nvbio::PackedStream<thrust::device_ptr, nvbio::uint8, 1U, true, nvbio::uint32>, IndexIterator=thrust::detail::normal_iterator<thrust::device_ptr>, SymbolType=nvbio::uint8]" /home/conor/nvbio/nvbio/strings/wavelet_tree.h(343): here instantiation of "nvbio::WaveletTreeStorage<SystemTag, IndexType, SymbolType>::plain_view_type nvbio::plain_view(nvbio::WaveletTreeStorage<SystemTag, IndexType, SymbolType> &) [with SystemTag=nvbio::device_tag, IndexType=nvbio::uint32, SymbolType=nvbio::uint8]" /home/conor/nvbio/nvbio-test/wavelet_test.cu(106): here

3 errors detected in the compilation of "/tmp/tmpxft_000021da_00000000-7_wavelet_test.cpp1.ii". CMake Error at nvbio-test_generated_wavelet_test.cu.o.cmake:264 (message): Error generating file /home/conor/nvbio/build/nvbio-test/CMakeFiles/nvbio-test.dir//./nvbio-test_generated_wavelet_test.cu.o

make[2]: * [nvbio-test/CMakeFiles/nvbio-test.dir/./nvbio-test_generated_wavelet_test.cu.o] Error 1 make[1]: * [nvbio-test/CMakeFiles/nvbio-test.dir/all] Error 2 make[1]: *\ Waiting for unfinished jobs.... /home/conor/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type" detected during: instantiation of class "nvbio::iterator_system [with iterator=thrust::device_ptrnvbio::uint32]" /home/conor/nvbio/nvbio/basic/packedstream_inl.h(1414): here instantiation of "void nvbio::assign(IndexType, InputIterator, nvbio::PackedStream<InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType>) [with InputIterator=thrust::transform_iteratornvbio::select_bit_functor<nvbio::uint8, thrust::detail::normal_iteratorthrust::device_ptr, thrust::use_default, thrust::use_default>, InputStream=thrust::device_ptrnvbio::uint32, Symbol=nvbio::uint8, SYMBOL_SIZE_T=1U, BIG_ENDIAN_T=true, IndexType=nvbio::uint32]" /home/conor/nvbio/nvbio/strings/wavelet_tree_inl.h(197): here instantiation of "void nvbio::setup(index_type, const string_iterator &, nvbio::WaveletTreeStorage<system_tag, index_type, symbol_type> &) [with system_tag=nvbio::device_tag, string_iterator=nvbio::PackedStreamthrust::device_ptr<nvbio::uint32, nvbio::uint8, 8U, true, nvbio::uint32>, index_type=nvbio::uint32, symbol_type=nvbio::uint8]" /home/conor/nvbio/examples/waveletfm/waveletfm.cu(93): here

3 errors detected in the compilation of "/tmp/tmpxft_000021e5_00000000-7_waveletfm.cpp1.ii". CMake Error at waveletfm_generated_waveletfm.cu.o.cmake:264 (message): Error generating file /home/conor/nvbio/build/examples/waveletfm/CMakeFiles/waveletfm.dir//./waveletfm_generated_waveletfm.cu.o

make[2]: * [examples/waveletfm/CMakeFiles/waveletfm.dir/./waveletfm_generated_waveletfm.cu.o] Error 1 make[1]: * [examples/waveletfm/CMakeFiles/waveletfm.dir/all] Error 2 1 error detected in the compilation of "/tmp/tmpxft_000021d2_00000000-7_haplotype_caller.cpp1.ii". CMake Error at nvMicroAssembly_generated_haplotype_caller.cu.o.cmake:264 (message): Error generating file /home/conor/nvbio/build/nvMicroAssembly/CMakeFiles/nvMicroAssembly.dir//./nvMicroAssembly_generated_haplotype_caller.cu.o

make[2]: * [nvMicroAssembly/CMakeFiles/nvMicroAssembly.dir/./nvMicroAssembly_generated_haplotype_caller.cu.o] Error 1 make[1]: * [nvMicroAssembly/CMakeFiles/nvMicroAssembly.dir/all] Error 2 make: *\ [all] Error 2

— Reply to this email directly or view it on GitHub https://github.com/NVlabs/nvbio/issues/11.

CnrLwlss commented 8 years ago

Aha! Sorry, I didn't spot that requirement. I've downgraded my CUDA installation to 6.5 and it compiles now. Thanks.